Related papers: Understanding the Systems Biology of Pathogen Viru…
In this paper, we present a toolbox for a specific optimization problem that frequently arises in bioinformatics or genomics. In this specific optimisation problem, the state space is a set of words of specified length over a finite…
Computational pathology demands both visual pattern recognition and dynamic integration of structured domain knowledge, including taxonomy, grading criteria, and clinical evidence. In practice, diagnostic reasoning requires linking…
Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are also emerging as a valuable avenue for predicting, understanding and…
In recent years, there has been an increased focus on early detection, prevention, and prediction of diseases. This, together with advances in sensor technology and the Internet of Things, has led to accelerated efforts in the development…
Medical imaging diagnosis increasingly relies on Machine Learning (ML) models. This is a task that is often hampered by severely imbalanced datasets, where positive cases can be quite rare. Their use is further compromised by their limited…
Histology analysis of the tumor micro-environment integrated with genomic assays is the gold standard for most cancers in modern medicine. This paper proposes a Gene-induced Multimodal Pre-training (GiMP) framework, which jointly…
In this paper, we propose applying semantic embedding to learn the range of behaviors exhibited by molecular swarms, thereby providing a richer set of features to optimize such systems. Specifically, we consider a standard molecular swarm…
The developing field of enhanced diagnostic techniques in the diagnosis of infectious diseases, constitutes a crucial domain in modern healthcare. By utilizing Gas Chromatography-Ion Mobility Spectrometry (GC-IMS) data and incorporating…
Marine biodiversity monitoring requires scalability and reliability across complex underwater environments to support conservation and invasive-species management. Yet existing detection solutions often exhibit a pronounced deployment gap,…
This paper reports on experience with using semantically-enabled network resource models to construct an operational multi-domain networked infrastructure-as-a-service (NIaaS) testbed called ExoGENI, recently funded through NSF's GENI…
Multimodal pathological image understanding has garnered widespread interest due to its potential to improve diagnostic accuracy and enable personalized treatment through integrated visual and textual data. However, existing methods exhibit…
Examining individual components of cellular systems has been successful in uncovering molecular reactions and interactions. However, the challenge lies in integrating these components into a comprehensive system-scale map. This difficulty…
In order to fully harness the potential of machine learning, it is crucial to establish a system that renders the field more accessible and less daunting for individuals who may not possess a comprehensive understanding of its intricacies.…
Interpreting gene clusters from RNA sequencing (RNA-seq) remains challenging, especially in antimicrobial resistance studies where mechanistic insight is important for hypothesis generation. Existing pathway enrichment methods can summarize…
The biomedical literature contains a vast collection of omics studies, yet most published data remain functionally inaccessible for computational reuse. When raw data are deposited in public repositories, essential information for…
Viruses are submicroscopic agents that can infect all kinds of lifeforms and use their hosts' living cells to replicate themselves. Despite having some of the simplest genetic structures among all living beings, viruses are highly…
The present work is inscribed within the intersection of two scientific thematic: the engineering by reuse of components and ontologies alignment. The integration of Business Components (BC) is a research problem that has been identified in…
Tools to explore scientific literature are essential for scientists, especially in biomedicine, where about a million new papers are published every year. Many such tools provide users the ability to search for specific entities (e.g.…
The rise of Artificial Intelligence creates great promise in the field of medical discovery, diagnostics and patient management. However, the vast complexity of all medical domains require a more complex approach that combines machine…
We propose orthogonal inductive matrix completion (OMIC), an interpretable approach to matrix completion based on a sum of multiple orthonormal side information terms, together with nuclear-norm regularization. The approach allows us to…